[Biopython] Helpa Newbie Please.py

[Willis, Jordan R]

Hi Gary,

Python will always look for the file in whichever directory you started python in. I would go to the command line and start python in the same directory in which you have ls_orchid.gbk.

On another note, I'm not sure when this changed but SeqIO.parse will only accept a file object contrary to the example. So try this.

from Bio import SeqIO
for seq_record in SeqIO.parse(open("ls_orchid.gbk"), "genbank"):
    print seq_record.id
    print repr(seq_record.seq)
   print len(seq_record)

Jordan

On 6/6/10 6:24 PM, "Gary" <gnd9 at cox.net> wrote:

Subject: Helpa Newbie Please.py


Just started into this fantastic project & can't get past Cookbook 2.4.2 parsing example!

from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.gbk", "genbank"):
    print seq_record.id
    print repr(seq_record.seq)
    print len(seq_record)

ALWAYS REPLYS:

Traceback (most recent call last):
File "(stdin)"' line1, in (module)
File "C:\Python26\lib\site-package\Bio\SeqIO\_init_.py"' line 483, in parse
IOError: [Error 2] No such file or directory: 'ls_orchid.gbk'


I do have the file in fact I put it in several locations.... genbank folder, SeqIO folder, Python2.6 folder....
Does anyone know which folder SeqIO is looking for the orchid file?
I assume thats my problem

Thanks in advance
Helpa Newbie Please.py




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